Paul Allen's Digital Brain

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Paul Allen's Digital Brain

SEATTLE – Whether they're at a university, a pharmaceutical company or in high school, scientists around the world now have an intricate digital atlas of the brain at their fingertips.

Scientists have mapped every gene in the mouse brain as part of Paul Allen's Brain Atlas project launched in 2003. While brain maps until now have been similar to a traditional encyclopedia, the Allen Brain Atlas is more like Google Earth.

When the Microsoft co-founder donated $100 million for the project, his stipulations were that the map be open access and free.

"The brain is one of the richest green fields of science," Allen told Wired News. "There's so much yet to be discovered. So I brought together a group of scientists and asked them to tell me what could be done that wasn’t yet being done – something that could be accomplished within a reasonable number of years and advance the whole field."

The idea to construct a database analysis of the mouse brain surfaced early on in those conversations, and the idea stuck. Researchers chose to work with mouse tissue instead of human samples because both share many genetic similarities, and mouse tissue is far less expensive and more easily obtained.

The brain atlas combines cellular-resolution scans of the mouse brain with precise information about which genes are expressed where.

"We have essentially mapped each individual gene in the mouse brain, about 21,000 genes in all, down to the cellular level," said Allan Jones, chief scientific officer at the Allen Institute for Brain Science.

The brains of mice and men are not genetically identical, however – tiny differences produce very different brains. For this reason, the institute's next project will map human brain samples in an effort to better understand human neurological health and disease.

Jones and his colleagues gathered approximately 650 terabytes of raw data, including 85 million photo tiles of ultra-thin slices of mouse brain tissue.

"If that were on magnetic tape that would be about 300 miles worth," said Jones. "And from this data, we have determined that about 80 percent of all genes are turned on somewhere in the brain. Before, scientists generally thought that number was closer to 60 or 70 percent."

The Allen Institute sits above a canal that leads to the Puget Sound in a quiet Seattle neighborhood. Inside the lab, row after row of sophisticated machines transform once-living tissue into digital information to build the Atlas. Machines seem to outnumber the people in white lab coats here, and Paul Allen says the link between human and machine intelligence is part of what inspired him to fund the project.

"If you came up through computer engineering and software like I did, the fact that the human brain works in such a different fashion than computers, and does so many things better than computers do (is fascinating)," said Allen.

About 250 scientists log on each day lately, according to institute directors, and they are already learning new things.

"One researcher at Harvard who studies obesity found a receptor in the hypothalamus, an area involved in appetite and feeding control," said Allen. "Subsequently, he built a research program around this finding. It's really rewarding for me – every time I travel to various scientific institutions, I pick up stories where people say 'I used this data in this way and it changed the direction of my research.'"

Half of the initial $100 million Allen donated to the Institute in 2003 was earmarked for the Allen Brain Atlas, which was completed under budget with $9 million to spare. The nonprofit’s directors plan to use the remaining $59 million to continue Institute operations in years to come, and will seek additional sources of public and private funding for the next big step: scanning human brain tissue.